Physical mutagenesis with 60 Co is a technique used in plant breeding to induce desired phenotypic characteristics. This research objective was to evaluate physical and physiological quality and protein content of jalapeño pepper (Capsicum annuum L.) seeds from plants that were selected as tolerant to water stress, these plants were derived from seeds irradiated with 60 Co at 100 Gy dose (T1P2 and T1P5 both from tolerant plants to water stress). Control seeds were significantly superior to the mutants in the variable standard germination (90.66%), standard germination with accelerated aging (57.3%), normal seedlings (95.6%), 1000 seeds weight (6.349 g), hectoliter weight (51.97 kg hL -1 ) and radicle dry weight (18 mg). Mutant seeds were significantly superior to control seeds in seed length and width (4.356 mm in T1P2 and 4.256 mm in T1P5 for length; 3.544 mm in T1P2 and 3.632 mm in T1P5 for width). In seed thickness tests, germinated seeds aerial part fresh and dry weight, radicle fresh weight, the two mutants seed types and the control were significantly equal. In seed storage proteins content, T1P2 treatment had a higher globulins concentration. In the prolamin fraction, the two mutant seed types were superior to control. T1P5 treatment seeds had the highest glutelins concentration. Mutant seeds showed different characteristics as compared to control in physical, physiological and plantlet parts weight components.